Jira suddenly closes and creates hs_err_pid.log file

Whenever i'm going to start JIRA it creates hs_err_pid.log file at installation directory and suddenly closing off the JIRA.

Is anybody face this issue ???Please let me know how can i resolve this issue and why this error was getting me.

i'm Using JIra 7.1.2v and Jdk 1.8v.

attached hs_err_pid.log file.

1 answer

0 vote

What do the application logs say about the error at this time?   My guess is you've not allowed it enough memory, but before acting on that, check the application logs (<JIRA home>/log/atlassian-jira.log and <JIRA install>/logs/catalina.out are the usual ones)

Hi Nic

in both catalina.out and atlassian-jira.log file, got the warning only

 

cataline.out 

12-Sep-2016 14:51:24.320 WARNING [http-nio-8088-exec-21] com.sun.jersey.spi.container.servlet.WebComponent.filterFormParameters A servlet request, to the URI http://localhost:8088/jira/rest/gadget/1.0/login, contains form parameters in the request body but the request body has been consumed by the servlet or a servlet filter accessing the request parameters. Only resource methods using @FormParam will work as expected. Resource methods consuming the request body by other means will not work as expected.

atlassian-jira.log 

2016-09-12 16:13:35,903 ThreadPoolAsyncTaskExecutor::Thread 4 WARN      [o.s.b.factory.support.DefaultListableBeanFactory] Overriding user-defined bean definition for bean 'clock' with a framework-generated bean definition: replacing [Generic bean: class [com.atlassian.plugin.osgi.bridge.external.HostComponentFactoryBean]; scope=; abstract=false; lazyInit=true; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [bundle://71.0:0/META-INF/spring/atlassian-plugins-host-components.xml]] with [Root bean: class [org.eclipse.gemini.blueprint.service.importer.support.OsgiServiceProxyFactoryBean]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null]
2016-09-12 16:13:36,011 ThreadPoolAsyncTaskExecutor::Thread 4 WARN      [o.s.b.factory.support.DefaultListableBeanFactory] Overriding user-defined bean definition for bean 'applicationProperties' with a framework-generated bean definition: replacing [Generic bean: class [com.atlassian.plugin.osgi.bridge.external.HostComponentFactoryBean]; scope=; abstract=false; lazyInit=true; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [bundle://71.0:0/META-INF/spring/atlassian-plugins-host-components.xml]] with [Root bean: class [org.eclipse.gemini.blueprint.service.importer.support.OsgiServiceProxyFactoryBean]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null]
2016-09-12 16:13:36,040 ThreadPoolAsyncTaskExecutor::Thread 4 WARN      [o.s.b.factory.support.DefaultListableBeanFactory] Overriding user-defined bean definition for bean 'jiraLicenseManager' with a framework-generated bean definition: replacing [Generic bean: class [com.atlassian.plugin.osgi.bridge.external.HostComponentFactoryBean]; scope=; abstract=false; lazyInit=true; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [bundle://71.0:0/META-INF/spring/atlassian-plugins-host-components.xml]] with [Root bean: class [org.eclipse.gemini.blueprint.service.importer.support.OsgiServiceProxyFactoryBean]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null]
2016-09-12 16:13:36,051 ThreadPoolAsyncTaskExecutor::Thread 4 WARN      [o.s.b.factory.support.DefaultListableBeanFactory] Overriding user-defined bean definition for bean 'mailSettings' with a framework-generated bean definition: replacing [Generic bean: class [com.atlassian.plugin.osgi.bridge.external.HostComponentFactoryBean]; scope=; abstract=false; lazyInit=true; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [bundle://71.0:0/META-INF/spring/atlassian-plugins-host-components.xml]] with [Root bean: class [org.eclipse.gemini.blueprint.service.importer.support.OsgiServiceProxyFactoryBean]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null]
2016-09-12 16:13:36,053 ThreadPoolAsyncTaskExecutor::Thread 4 WARN      [o.s.b.factory.support.DefaultListableBeanFactory] Overriding user-defined bean definition for bean 'jiraWebResourceManager' with a framework-generated bean definition: replacing [Generic bean: class [com.atlassian.plugin.osgi.bridge.external.HostComponentFactoryBean]; scope=; abstract=false; lazyInit=true; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [bundle://71.0:0/META-INF/spring/atlassian-plugins-host-components.xml]] with [Root bean: class [org.eclipse.gemini.blueprint.service.importer.support.OsgiServiceProxyFactoryBean]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null]
2016-09-12 16:13:36,056 ThreadPoolAsyncTaskExecutor::Thread 4 WARN      [o.s.b.factory.support.DefaultListableBeanFactory] Overriding user-defined bean definition for bean 'globalPermissionManager' with a framework-generated bean definition: replacing [Generic bean: class [com.atlassian.plugin.osgi.bridge.external.HostComponentFactoryBean]; scope=; abstract=false; lazyInit=true; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [bundle://71.0:0/META-INF/spring/atlassian-plugins-host-components.xml]] with [Root bean: class [org.eclipse.gemini.blueprint.service.importer.support.OsgiServiceProxyFactoryBean]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null]
2016-09-12 16:13:36,060 ThreadPoolAsyncTaskExecutor::Thread 4 WARN      [o.s.b.factory.support.DefaultListableBeanFactory] Overriding user-defined bean definition for bean 'jiraAuthenticationContext' with a framework-generated bean definition: replacing [Generic bean: class [com.atlassian.plugin.osgi.bridge.external.HostComponentFactoryBean]; scope=; abstract=false; lazyInit=true; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [bundle://71.0:0/META-INF/spring/atlassian-plugins-host-components.xml]] with [Root bean: class [org.eclipse.gemini.blueprint.service.importer.support.OsgiServiceProxyFactoryBean]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null]
2016-09-12 16:13:36,065 ThreadPoolAsyncTaskExecutor::Thread 4 WARN      [o.s.b.factory.support.DefaultListableBeanFactory] Overriding user-defined bean definition for bean 'systemInfoUtils' with a framework-generated bean definition: replacing [Generic bean: class [com.atlassian.plugin.osgi.bridge.external.HostComponentFactoryBean]; scope=; abstract=false; lazyInit=true; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [bundle://71.0:0/META-INF/spring/atlassian-plugins-host-components.xml]] with [Root bean: class [org.eclipse.gemini.blueprint.service.importer.support.OsgiServiceProxyFactoryBean]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null]
2016-09-12 16:13:36,067 ThreadPoolAsyncTaskExecutor::Thread 4 WARN      [o.s.b.factory.support.DefaultListableBeanFactory] Overriding user-defined bean definition for bean 'mailServerManager' with a framework-generated bean definition: replacing [Generic bean: class [com.atlassian.plugin.osgi.bridge.external.HostComponentFactoryBean]; scope=; abstract=false; lazyInit=true; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [bundle://71.0:0/META-INF/spring/atlassian-plugins-host-components.xml]] with [Root bean: class [org.eclipse.gemini.blueprint.service.importer.support.OsgiServiceProxyFactoryBean]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null]
2016-09-12 16:13:39,552 ThreadPoolAsyncTaskExecutor::Thread 5 INFO      [c.a.p.s.scanner.util.ProductFilterUtil] Detected product: JIRA
2016-09-12 16:13:47,672 ThreadPoolAsyncTaskExecutor::Thread 18 DEBUG      [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] afterPropertiesSet

Is that literally the end of both logs, just where it stops dead?

and one more thing is, i'm using same JIRA verion from last six months i could not faced this problem previous, i'm facing this problem from last one week that time i deleted the bundled plugins and osgi plugins from <jira_Home/plugins> directory after that it works fine.

but unfortunetly today i'm facing same problem.

yes.

for seeing the fresh log details i was tring to start JIRA again now  its started successfully and works.

i'm attaching catalina file 

and in atlassian.log file i got the following error

2016-09-12 16:45:29,381 pool-29-thread-1 ERROR      [c.s.l.t.connector.rest.RestClientImpl] Unexpected error
java.net.ConnectException: Connection refused: connect
	at java.net.DualStackPlainSocketImpl.waitForConnect(Native Method)
	at java.net.DualStackPlainSocketImpl.socketConnect(Unknown Source)
	at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source)
	at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source)
	at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
	at java.net.PlainSocketImpl.connect(Unknown Source)
	at java.net.SocksSocketImpl.connect(Unknown Source)
	at java.net.Socket.connect(Unknown Source)
	... 3 filtered
	at java.lang.reflect.Method.invoke(Unknown Source)
	at org.apache.commons.httpclient.protocol.ReflectionSocketFactory.createSocket(ReflectionSocketFactory.java:140)
	at org.apache.commons.httpclient.protocol.DefaultProtocolSocketFactory.createSocket(DefaultProtocolSocketFactory.java:125)
	at org.apache.commons.httpclient.HttpConnection.open(HttpConnection.java:707)
	at org.apache.commons.httpclient.MultiThreadedHttpConnectionManager$HttpConnectionAdapter.open(MultiThreadedHttpConnectionManager.java:1361)
	at org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDirector.java:387)
	at org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:171)
	at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397)
	at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:346)
	at com.stiltsoft.lib.teamcity.connector.rest.RestClientImpl.execute(RestClientImpl.java:185)
	at com.stiltsoft.lib.teamcity.connector.rest.RestClientImpl.get(RestClientImpl.java:94)
	at com.stiltsoft.lib.teamcity.connector.rest.RestClientImpl.get(RestClientImpl.java:108)
	at com.stiltsoft.lib.teamcity.connector.rest.DefaultTeamCityManager.getBuildsRef(DefaultTeamCityManager.java:229)
	at com.stiltsoft.lib.teamcity.connector.rest.DefaultTeamCityManager.getOnlyBuilds(DefaultTeamCityManager.java:192)
	at com.stiltsoft.jira.extra.teamcity.index.update.IndexUpdaterImpl.invoke(IndexUpdaterImpl.java:64)
	at com.stiltsoft.jira.extra.teamcity.service.lock.AbstractLockedRunnable.run(AbstractLockedRunnable.java:31)
	at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)

Ok, that looks like some form of connector error - an add-on that's talking to Team City.

But, you're giving us snippets of log here, ones that I think you think are a problem.  Could you simply give us the couple of hundred lines that were generated at the time of the crash, and leading up to it?

yes Nic, that was connector error because right now i could not running TeamCity.

but sometimes it works and sometimes not..

latest atlassian-jira.log file details.

2016-09-12 17:20:10,468 JIRA-Bootstrap DEBUG      [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] getService bundle [com.pyxis.greenhopper.jira]
2016-09-12 17:20:11,127 JIRA-Bootstrap INFO      [atlassian.plugin] eazyBI: schedule initializer
2016-09-12 17:20:11,283 JIRA-Bootstrap DEBUG      [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] getService bundle [com.thed.zephyr.je]
2016-09-12 17:20:11,315 JIRA-Bootstrap INFO      [c.a.j.p.e.bamboo.service.PlanStatusUpdateServiceImpl] PlanStatusUpdateJob scheduled to run every 60 seconds
2016-09-12 17:20:11,315 JIRA-Bootstrap DEBUG      [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] getService bundle [com.xiplink.jira.git.jira_git_plugin]
2016-09-12 17:20:16,883 JIRA-Bootstrap INFO      [c.a.j.i.fields.option.OptionSetPersisterImpl] All options removed for config id13300
2016-09-12 17:20:17,750 JIRA-Bootstrap INFO      [c.a.j.i.fields.option.OptionSetPersisterImpl] All options removed for config id13301
2016-09-12 17:20:19,317 JIRA-Bootstrap DEBUG      [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] getService bundle [com.stiltsoft.jira.teamcity.jira-teamcity-plugin]
2016-09-12 17:20:19,792 JIRA-Bootstrap DEBUG      [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] getService bundle [com.atlassian.jira.plugins.webhooks.jira-webhooks-plugin]
2016-09-12 17:20:24,488 JIRA-Bootstrap INFO      [c.a.j.p.dvcs.scheduler.DvcsScheduler] DvcsScheduler job handler registered
2016-09-12 17:20:24,488 WaitForAO DEBUG      [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] getService bundle [com.atlassian.jira.plugins.jira-dvcs-connector-plugin]
2016-09-12 17:20:25,051 JIRA-Bootstrap INFO      [c.a.jira.scheduler.JiraSchedulerLauncher] Starting the JIRA Scheduler....
2016-09-12 17:20:25,222 JIRA-Bootstrap INFO      [c.a.jira.scheduler.JiraSchedulerLauncher] JIRA Scheduler started.
2016-09-12 17:20:27,171 Caesium-1-3 DEBUG ServiceRunner     [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] getService bundle [com.deiser.jira.profields]
2016-09-12 17:20:27,218 Caesium-1-1 INFO      [atlassian.plugin] eazyBI: initializer started
2016-09-12 17:20:29,960 pool-29-thread-1 ERROR      [c.s.l.t.connector.rest.RestClientImpl] Unexpected error
java.net.ConnectException: Connection refused: connect
	at java.net.DualStackPlainSocketImpl.waitForConnect(Native Method)
	at java.net.DualStackPlainSocketImpl.socketConnect(Unknown Source)
	at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source)
	at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source)
	at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
	at java.net.PlainSocketImpl.connect(Unknown Source)
	at java.net.SocksSocketImpl.connect(Unknown Source)
	at java.net.Socket.connect(Unknown Source)
	... 3 filtered
	at java.lang.reflect.Method.invoke(Unknown Source)
	at org.apache.commons.httpclient.protocol.ReflectionSocketFactory.createSocket(ReflectionSocketFactory.java:140)
	at org.apache.commons.httpclient.protocol.DefaultProtocolSocketFactory.createSocket(DefaultProtocolSocketFactory.java:125)
	at org.apache.commons.httpclient.HttpConnection.open(HttpConnection.java:707)
	at org.apache.commons.httpclient.MultiThreadedHttpConnectionManager$HttpConnectionAdapter.open(MultiThreadedHttpConnectionManager.java:1361)
	at org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDirector.java:387)
	at org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:171)
	at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397)
	at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:346)
	at com.stiltsoft.lib.teamcity.connector.rest.RestClientImpl.execute(RestClientImpl.java:185)
	at com.stiltsoft.lib.teamcity.connector.rest.RestClientImpl.get(RestClientImpl.java:94)
	at com.stiltsoft.lib.teamcity.connector.rest.RestClientImpl.get(RestClientImpl.java:108)
	at com.stiltsoft.lib.teamcity.connector.rest.DefaultTeamCityManager.getBuildsRef(DefaultTeamCityManager.java:229)
	at com.stiltsoft.lib.teamcity.connector.rest.DefaultTeamCityManager.getOnlyBuilds(DefaultTeamCityManager.java:192)
	at com.stiltsoft.jira.extra.teamcity.index.update.IndexUpdaterImpl.invoke(IndexUpdaterImpl.java:64)
	at com.stiltsoft.jira.extra.teamcity.service.lock.AbstractLockedRunnable.run(AbstractLockedRunnable.java:31)
	at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
2016-09-12 17:20:29,960 pool-29-thread-1 ERROR      [c.s.j.e.t.index.update.IndexUpdaterImpl] Unable to synchronize with TeamCity TeamCity
java.net.ConnectException: Connection refused: connect
	at java.net.DualStackPlainSocketImpl.waitForConnect(Native Method)
	at java.net.DualStackPlainSocketImpl.socketConnect(Unknown Source)
	at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source)
	at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source)
	at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
	at java.net.PlainSocketImpl.connect(Unknown Source)
	at java.net.SocksSocketImpl.connect(Unknown Source)
	at java.net.Socket.connect(Unknown Source)
	... 3 filtered
	at java.lang.reflect.Method.invoke(Unknown Source)
	at org.apache.commons.httpclient.protocol.ReflectionSocketFactory.createSocket(ReflectionSocketFactory.java:140)
	at org.apache.commons.httpclient.protocol.DefaultProtocolSocketFactory.createSocket(DefaultProtocolSocketFactory.java:125)
	at org.apache.commons.httpclient.HttpConnection.open(HttpConnection.java:707)
	at org.apache.commons.httpclient.MultiThreadedHttpConnectionManager$HttpConnectionAdapter.open(MultiThreadedHttpConnectionManager.java:1361)
	at org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDirector.java:387)
	at org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:171)
	at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397)
	at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:346)
	at com.stiltsoft.lib.teamcity.connector.rest.RestClientImpl.execute(RestClientImpl.java:185)
	at com.stiltsoft.lib.teamcity.connector.rest.RestClientImpl.get(RestClientImpl.java:94)
	at com.stiltsoft.lib.teamcity.connector.rest.RestClientImpl.get(RestClientImpl.java:108)
	at com.stiltsoft.lib.teamcity.connector.rest.DefaultTeamCityManager.getBuildsRef(DefaultTeamCityManager.java:229)
	at com.stiltsoft.lib.teamcity.connector.rest.DefaultTeamCityManager.getOnlyBuilds(DefaultTeamCityManager.java:192)
	at com.stiltsoft.jira.extra.teamcity.index.update.IndexUpdaterImpl.invoke(IndexUpdaterImpl.java:64)
	at com.stiltsoft.jira.extra.teamcity.service.lock.AbstractLockedRunnable.run(AbstractLockedRunnable.java:31)
	at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
2016-09-12 17:20:31,593 Caesium-1-1 INFO      [atlassian.plugin] eazyBI: initializer completed
2016-09-12 17:20:33,648 JIRA-Bootstrap INFO      [c.a.j.index.ha.DefaultIndexRecoveryManager] Latest index date: {2016-09-07 13:26:07}, Latest DB date: {2016-09-07 13:26:07}
2016-09-12 17:20:37,810 JIRA-Bootstrap DEBUG      [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] getService bundle [com.marvelution.jira.plugins.jenkins]
2016-09-12 17:20:38,226 UpmScheduler:thread-1 WARN anonymous     [c.a.upm.pac.PacClientImpl] Timed out while checking for addon updates: com.atlassian.util.concurrent.RuntimeTimeoutException: com.atlassian.util.concurrent.TimedOutException: Timed out after: 10000000000 NANOSECONDS
2016-09-12 17:20:38,508 JIRA-Bootstrap INFO      [c.a.jira.startup.DefaultInstantUpgradeManager] Late startup launchers took 56s
2016-09-12 17:20:38,555 JIRA Warmer Thread:thread-1 INFO      [c.a.jira.i18n.I18nWarmer] Init i18n cache
2016-09-12 17:20:38,586 JIRA-Bootstrap INFO      [c.a.jira.startup.LauncherContextListener] Memory Usage:
    ---------------------------------------------------------------------------------
      Heap memory     :  Used:  505 MiB.  Committed:  729 MiB.  Max:  974 MiB
      Non-heap memory :  Used:  277 MiB.  Committed:  300 MiB.  Max: 1264 MiB
    ---------------------------------------------------------------------------------
      TOTAL           :  Used:  782 MiB.  Committed: 1028 MiB.  Max: 2238 MiB
    ---------------------------------------------------------------------------------
2016-09-12 17:20:43,084 JIRA Warmer Thread:thread-1 INFO      [c.a.jira.i18n.I18nWarmer] Initialised i18n cache in 4529
2016-09-12 17:21:03,745 hipchat-plugin-tasks-executor-0 DEBUG      [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] getService bundle [com.atlassian.plugins.base-hipchat-integration-plugin-api]
2016-09-12 17:21:11,863 Caesium-1-4 DEBUG      [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] getService bundle [com.atlassian.support.healthcheck.support-healthcheck-plugin]
2016-09-12 17:21:13,004 JenkinsConnectorExecutorServiceThread:thread-1 ERROR      [o.m.j.p.j.services.impl.RestCommunicator] Failed to connect to Jenkins [http://localhost:8001/]; org.apache.http.conn.HttpHostConnectException: Connect to localhost:8001 [localhost/127.0.0.1, localhost/0:0:0:0:0:0:0:1] failed: Connection refused: connect
com.atlassian.sal.api.net.ResponseException: org.apache.http.conn.HttpHostConnectException: Connect to localhost:8001 [localhost/127.0.0.1, localhost/0:0:0:0:0:0:0:1] failed: Connection refused: connect
	at com.atlassian.sal.core.net.HttpClientRequest.executeAndReturn(HttpClientRequest.java:119)
	at org.marvelution.jira.plugins.jenkins.services.impl.RestCommunicator.executeRequest(RestCommunicator.java:417)
	at org.marvelution.jira.plugins.jenkins.services.impl.RestCommunicator.createAndExecuteRequest(RestCommunicator.java:405)
	at org.marvelution.jira.plugins.jenkins.services.impl.RestCommunicator.getRemoteStatus(RestCommunicator.java:92)
	at org.marvelution.jira.plugins.jenkins.sync.impl.AbstractCommunicatorAwareSynchronizationOperation.synchronize(AbstractCommunicatorAwareSynchronizationOperation.java:46)
	at org.marvelution.jira.plugins.jenkins.sync.impl.DefaultSynchronizer.lambda$scheduleInternal$0(DefaultSynchronizer.java:95)
	at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
Caused by: org.apache.http.conn.HttpHostConnectException: Connect to localhost:8001 [localhost/127.0.0.1, localhost/0:0:0:0:0:0:0:1] failed: Connection refused: connect
	at org.apache.http.impl.conn.DefaultHttpClientConnectionOperator.connect(DefaultHttpClientConnectionOperator.java:151)
	at org.apache.http.impl.conn.PoolingHttpClientConnectionManager.connect(PoolingHttpClientConnectionManager.java:353)
	at org.apache.http.impl.execchain.MainClientExec.establishRoute(MainClientExec.java:380)
	at org.apache.http.impl.execchain.MainClientExec.execute(MainClientExec.java:236)
	at org.apache.http.impl.execchain.ProtocolExec.execute(ProtocolExec.java:184)
	at org.apache.http.impl.execchain.RedirectExec.execute(RedirectExec.java:110)
	at org.apache.http.impl.client.InternalHttpClient.doExecute(InternalHttpClient.java:184)
	at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
	at com.atlassian.sal.core.net.HttpClientRequest.executeAndReturn(HttpClientRequest.java:109)
	... 10 more
Caused by: java.net.ConnectException: Connection refused: connect
	at java.net.DualStackPlainSocketImpl.waitForConnect(Native Method)
	at java.net.DualStackPlainSocketImpl.socketConnect(Unknown Source)
	at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source)
	at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source)
	at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
	at java.net.SocksSocketImpl.connect(Unknown Source)
	at java.net.Socket.connect(Unknown Source)
	at org.apache.http.conn.socket.PlainConnectionSocketFactory.connectSocket(PlainConnectionSocketFactory.java:74)
	at org.apache.http.impl.conn.DefaultHttpClientConnectionOperator.connect(DefaultHttpClientConnectionOperator.java:134)
	... 19 more
2016-09-12 17:21:28,972 pool-29-thread-1 ERROR      [c.s.l.t.connector.rest.RestClientImpl] Unexpected error
java.net.ConnectException: Connection refused: connect
	at java.net.DualStackPlainSocketImpl.waitForConnect(Native Method)
	at java.net.DualStackPlainSocketImpl.socketConnect(Unknown Source)
	at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source)
	at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source)
	at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
	at java.net.PlainSocketImpl.connect(Unknown Source)
	at java.net.SocksSocketImpl.connect(Unknown Source)
	at java.net.Socket.connect(Unknown Source)
	... 3 filtered
	at java.lang.reflect.Method.invoke(Unknown Source)
	at org.apache.commons.httpclient.protocol.ReflectionSocketFactory.createSocket(ReflectionSocketFactory.java:140)
	at org.apache.commons.httpclient.protocol.DefaultProtocolSocketFactory.createSocket(DefaultProtocolSocketFactory.java:125)
	at org.apache.commons.httpclient.HttpConnection.open(HttpConnection.java:707)
	at org.apache.commons.httpclient.MultiThreadedHttpConnectionManager$HttpConnectionAdapter.open(MultiThreadedHttpConnectionManager.java:1361)
	at org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDirector.java:387)
	at org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:171)
	at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397)
	at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:346)
	at com.stiltsoft.lib.teamcity.connector.rest.RestClientImpl.execute(RestClientImpl.java:185)
	at com.stiltsoft.lib.teamcity.connector.rest.RestClientImpl.get(RestClientImpl.java:94)
	at com.stiltsoft.lib.teamcity.connector.rest.RestClientImpl.get(RestClientImpl.java:108)
	at com.stiltsoft.lib.teamcity.connector.rest.DefaultTeamCityManager.getBuildsRef(DefaultTeamCityManager.java:229)
	at com.stiltsoft.lib.teamcity.connector.rest.DefaultTeamCityManager.getOnlyBuilds(DefaultTeamCityManager.java:192)
	at com.stiltsoft.jira.extra.teamcity.index.update.IndexUpdaterImpl.invoke(IndexUpdaterImpl.java:64)
	at com.stiltsoft.jira.extra.teamcity.service.lock.AbstractLockedRunnable.run(AbstractLockedRunnable.java:31)
	at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
2016-09-12 17:21:28,988 pool-29-thread-1 ERROR      [c.s.j.e.t.index.update.IndexUpdaterImpl] Unable to synchronize with TeamCity TeamCity
java.net.ConnectException: Connection refused: connect
	at java.net.DualStackPlainSocketImpl.waitForConnect(Native Method)
	at java.net.DualStackPlainSocketImpl.socketConnect(Unknown Source)
	at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source)
	at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source)
	at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
	at java.net.PlainSocketImpl.connect(Unknown Source)
	at java.net.SocksSocketImpl.connect(Unknown Source)
	at java.net.Socket.connect(Unknown Source)
	... 3 filtered
	at java.lang.reflect.Method.invoke(Unknown Source)
	at org.apache.commons.httpclient.protocol.ReflectionSocketFactory.createSocket(ReflectionSocketFactory.java:140)
	at org.apache.commons.httpclient.protocol.DefaultProtocolSocketFactory.createSocket(DefaultProtocolSocketFactory.java:125)
	at org.apache.commons.httpclient.HttpConnection.open(HttpConnection.java:707)
	at org.apache.commons.httpclient.MultiThreadedHttpConnectionManager$HttpConnectionAdapter.open(MultiThreadedHttpConnectionManager.java:1361)
	at org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDirector.java:387)
	at org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:171)
	at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397)
	at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:346)
	at com.stiltsoft.lib.teamcity.connector.rest.RestClientImpl.execute(RestClientImpl.java:185)
	at com.stiltsoft.lib.teamcity.connector.rest.RestClientImpl.get(RestClientImpl.java:94)
	at com.stiltsoft.lib.teamcity.connector.rest.RestClientImpl.get(RestClientImpl.java:108)
	at com.stiltsoft.lib.teamcity.connector.rest.DefaultTeamCityManager.getBuildsRef(DefaultTeamCityManager.java:229)
	at com.stiltsoft.lib.teamcity.connector.rest.DefaultTeamCityManager.getOnlyBuilds(DefaultTeamCityManager.java:192)
	at com.stiltsoft.jira.extra.teamcity.index.update.IndexUpdaterImpl.invoke(IndexUpdaterImpl.java:64)
	at com.stiltsoft.jira.extra.teamcity.service.lock.AbstractLockedRunnable.run(AbstractLockedRunnable.java:31)
	at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
2016-09-12 17:22:25,604 Modification Check:thread-1 INFO      [c.a.jira.startup.JiraStartupLogger] 
    
    ___ Modifications ___________________________
    
         Modified Files                                : com/atlassian/jira/web/action/JiraWebActionSupport.properties, jira-application.properties
         Removed Files                                 : None
    
2016-09-12 17:22:28,939 pool-29-thread-1 ERROR      [c.s.l.t.connector.rest.RestClientImpl] Unexpected error
java.net.ConnectException: Connection refused: connect
	at java.net.DualStackPlainSocketImpl.waitForConnect(Native Method)
	at java.net.DualStackPlainSocketImpl.socketConnect(Unknown Source)
	at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source)
	at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source)
	at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
	at java.net.PlainSocketImpl.connect(Unknown Source)
	at java.net.SocksSocketImpl.connect(Unknown Source)
	at java.net.Socket.connect(Unknown Source)
	... 3 filtered
	at java.lang.reflect.Method.invoke(Unknown Source)
	at org.apache.commons.httpclient.protocol.ReflectionSocketFactory.createSocket(ReflectionSocketFactory.java:140)
	at org.apache.commons.httpclient.protocol.DefaultProtocolSocketFactory.createSocket(DefaultProtocolSocketFactory.java:125)
	at org.apache.commons.httpclient.HttpConnection.open(HttpConnection.java:707)
	at org.apache.commons.httpclient.MultiThreadedHttpConnectionManager$HttpConnectionAdapter.open(MultiThreadedHttpConnectionManager.java:1361)
	at org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDirector.java:387)
	at org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:171)
	at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397)
	at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:346)
	at com.stiltsoft.lib.teamcity.connector.rest.RestClientImpl.execute(RestClientImpl.java:185)
	at com.stiltsoft.lib.teamcity.connector.rest.RestClientImpl.get(RestClientImpl.java:94)
	at com.stiltsoft.lib.teamcity.connector.rest.RestClientImpl.get(RestClientImpl.java:108)
	at com.stiltsoft.lib.teamcity.connector.rest.DefaultTeamCityManager.getBuildsRef(DefaultTeamCityManager.java:229)
	at com.stiltsoft.lib.teamcity.connector.rest.DefaultTeamCityManager.getOnlyBuilds(DefaultTeamCityManager.java:192)
	at com.stiltsoft.jira.extra.teamcity.index.update.IndexUpdaterImpl.invoke(IndexUpdaterImpl.java:64)
	at com.stiltsoft.jira.extra.teamcity.service.lock.AbstractLockedRunnable.run(AbstractLockedRunnable.java:31)
	at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
2016-09-12 17:22:28,939 pool-29-thread-1 ERROR      [c.s.j.e.t.index.update.IndexUpdaterImpl] Unable to synchronize with TeamCity TeamCity
java.net.ConnectException: Connection refused: connect
	at java.net.DualStackPlainSocketImpl.waitForConnect(Native Method)
	at java.net.DualStackPlainSocketImpl.socketConnect(Unknown Source)
	at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source)
	at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source)
	at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
	at java.net.PlainSocketImpl.connect(Unknown Source)
	at java.net.SocksSocketImpl.connect(Unknown Source)
	at java.net.Socket.connect(Unknown Source)
	... 3 filtered
	at java.lang.reflect.Method.invoke(Unknown Source)
	at org.apache.commons.httpclient.protocol.ReflectionSocketFactory.createSocket(ReflectionSocketFactory.java:140)
	at org.apache.commons.httpclient.protocol.DefaultProtocolSocketFactory.createSocket(DefaultProtocolSocketFactory.java:125)
	at org.apache.commons.httpclient.HttpConnection.open(HttpConnection.java:707)
	at org.apache.commons.httpclient.MultiThreadedHttpConnectionManager$HttpConnectionAdapter.open(MultiThreadedHttpConnectionManager.java:1361)
	at org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDirector.java:387)
	at org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:171)
	at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397)
	at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:346)
	at com.stiltsoft.lib.teamcity.connector.rest.RestClientImpl.execute(RestClientImpl.java:185)
	at com.stiltsoft.lib.teamcity.connector.rest.RestClientImpl.get(RestClientImpl.java:94)
	at com.stiltsoft.lib.teamcity.connector.rest.RestClientImpl.get(RestClientImpl.java:108)
	at com.stiltsoft.lib.teamcity.connector.rest.DefaultTeamCityManager.getBuildsRef(DefaultTeamCityManager.java:229)
	at com.stiltsoft.lib.teamcity.connector.rest.DefaultTeamCityManager.getOnlyBuilds(DefaultTeamCityManager.java:192)
	at com.stiltsoft.jira.extra.teamcity.index.update.IndexUpdaterImpl.invoke(IndexUpdaterImpl.java:64)
	at com.stiltsoft.jira.extra.teamcity.service.lock.AbstractLockedRunnable.run(AbstractLockedRunnable.java:31)
	at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)

And the crash happens at that point?  Does catlaina.out have anything in it at the crash time?

Nic, i seen this things within catalina file

in catalina i was seen these warnings and all..i copied only warnings instead of this every thing was fine...
12-Sep-2016 14:51:24.320 WARNING [http-nio-8088-exec-21] com.sun.jersey.spi.container.servlet.WebComponent.filterFormParameters A servlet request, to the URI http://localhost:8088/jira/rest/gadget/1.0/login, contains form parameters in the request body but the request body has been consumed by the servlet or a servlet filter accessing the request parameters. Only resource methods using @FormParam will work as expected. Resource methods consuming the request body by other means will not work as expected.
12-Sep-2016 16:12:23.156 SEVERE [main] org.apache.catalina.startup.Catalina.stopServer Could not contact localhost:8008. Tomcat may not be running.
12-Sep-2016 16:29:05.718 SEVERE [main] org.apache.catalina.startup.Catalina.stopServer Could not contact localhost:8008. Tomcat may not be running.
12-Sep-2016 16:29:05.723 SEVERE [main] org.apache.catalina.startup.Catalina.stopServer Catalina.stop: 
 java.net.ConnectException: Connection refused: connect
	at java.net.DualStackPlainSocketImpl.connect0(Native Method)
	at java.net.DualStackPlainSocketImpl.socketConnect(Unknown Source)
	at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source)
	at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source)
	at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
	at java.net.PlainSocketImpl.connect(Unknown Source)
	at java.net.SocksSocketImpl.connect(Unknown Source)
	at java.net.Socket.connect(Unknown Source)
	at java.net.Socket.connect(Unknown Source)
	at java.net.Socket.&lt;init&gt;(Unknown Source)
	at java.net.Socket.&lt;init&gt;(Unknown Source)
	at org.apache.catalina.startup.Catalina.stopServer(Catalina.java:450)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
	at java.lang.reflect.Method.invoke(Unknown Source)
	at org.apache.catalina.startup.Bootstrap.stopServer(Bootstrap.java:400)
	at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:487)


12-Sep-2016 16:55:40.054 WARNING [http-nio-8088-exec-21] com.sun.jersey.spi.container.servlet.WebComponent.filterFormParameters A servlet request, to the URI http://localhost:8088/jira/rest/teamcity/1.0/gadget/agents.json?_=1473679540045, contains form parameters in the request body but the request body has been consumed by the servlet or a servlet filter accessing the request parameters. Only resource methods using @FormParam will work as expected. Resource methods consuming the request body by other means will not work as expected.
12-Sep-2016 16:55:40.358 WARNING [http-nio-8088-exec-20] null.null A servlet request, to the URI http://localhost:8088/jira/rest/calendar-plugin/1.0/calendar/htmlcalendar.html?dateFieldName=customfield_10415&amp;displayVersions=true&amp;numOfIssueIcons=10&amp;context=gadget&amp;portletId=10400&amp;includeContainer=true&amp;projectId=11201&amp;_=1473679539808, contains form parameters in the request body but the request body has been consumed by the servlet or a servlet filter accessing the request parameters. Only resource methods using @FormParam will work as expected. Resource methods consuming the request body by other means will not work as expected.
12-Sep-2016 16:55:42.928 WARNING [http-nio-8088-exec-19] null.null A servlet request, to the URI http://localhost:8088/jira/rest/teamcity/1.0/builds/show-more-builds2/?key=NONE&amp;tabType=GADGET_TAB&amp;lastBuildId=9223372036854775807_load_9223372036854775807&amp;filter=tc-filter-build-project%3D0d6cad8c-88f0-301c-84d6-a7050eb3e27c%2524TestProject%26tc-caption-build-project%3Dnull&amp;_=1473679542920, contains form parameters in the request body but the request body has been consumed by the servlet or a servlet filter accessing the request parameters. Only resource methods using @FormParam will work as expected. Resource methods consuming the request body by other means will not work as expected.
12-Sep-2016 17:17:12.714 SEVERE [main] org.apache.catalina.startup.Catalina.stopServer Could not contact localhost:8008. Tomcat may not be running.

We need to see the full data of what happened just before the crash.  Not snippets, or pieces of logs you've selected from different times.

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